Two mutant alleles of the gene encoding electron transfer flavoprotein-ubiquinone oxidoreductase were identified and characterized in fibroblasts from a patient with glutaric acidemia type II. One of these alleles is a C-T transition in the donor site of an intron that causes skipping of a 222 bp exon. Included in the missing 74 amino acids is C561, which is predicted to be one of the four cysteine ligands of the 4Fe4S cluster. This mutant allele does not encode a stable ETF-QO in human fibroblasts but, when expressed in Saccharomyces cerevisiae, the mutant ETF-QO is relatively stable and properly targeted to and processed by mitochondria. The mutant protein lacks ubiquinone reductase activity, but does accept electrons from ETF in the catalyzed disproportionation of ETF semiquinone. These data suggest that in the normal protein the flavin center accepts electrons from ETF and that the 4Fe4S cluster reduces ubiquinone. Deleting the 74 amino acids also alters the association between the protein and membrane such that the mutant ETF-QO cannot be extracted from the membrane using the same conditions used for wild type ETF-QO. A site directed mutant that contains only the single amino acid substitution, C561A, exhibits the same catalytic behavior as the deletion mutant, supporting the hypothesis regarding the specific functions of the two redox centers. It is, however, solubilized by the same conditions as wild type ETF-QO.